18,000 TF reporters were transfected into HepG2 and K562 cells (in total 6 different conditions), sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.
## barcode tf promoter
## 1246 TCCATCTAAGCG Trp53 mCMV
## 1768 CCACGATAGTAA Trp53 hBGm
## 2178 TGGTGAGCAATT Trp53 mCMV
## 2246 AGCAATAAGCCA Trp53 mCMV
## 3361 CGCCACAGTGTA Trp53 mCMV
## 3541 AACAGGCGGTCT Trp53 mCMV
## 3547 GCTCTCGAATTA Trp53 mCMV
## 3703 GTCTGTTCGATT Trp53 mCMV
## 3797 CTATTCTGTGCA Trp53 mCMV
## 4358 AACAGAACAAGG Trp53 mCMV
## 5109 TGGTGTAGCAGA Trp53 mCMV
## 5243 CAGCGACTGACA Trp53 mCMV
## 5305 CGATATAGCCAG Trp53 mCMV
## 5396 GCTCTACACGAG Trp53 mCMV
## 5655 CAAGGTATAGGA Trp53 mCMV
## 6927 TCGACCGGATTG Trp53 mCMV
## 7270 TCTCTCAGCGAA Trp53 hBGm
## 7359 ATCACTGTATCC Trp53 mCMV
## 7509 TGTAAGGTAGAG Trp53 mCMV
## 7883 TGGATTGAGACA Trp53 mCMV
## 8326 TCCGTAGCTTCC Trp53 mCMV
## 8358 TGTTCCTGTCTG Trp53 hBGm
## 9777 GAATAGACGGTG Trp53 mCMV
## 10215 CTTGACTCGCTG Trp53 mCMV
## 10606 TACAGCGTTACC Trp53 hBGm
## 10763 ATACTCGTTCGC Trp53 mCMV
## 11459 ACTCCGTATTGC Trp53 mCMV
## 11820 GTTCGAAGCTCA Trp53 mCMV
## 12698 CGTTCGGAGAGA Trp53 mCMV
## 12939 ACCTCTTAGGTC Trp53 mCMV
## 13232 CGTTGAATATCG Trp53 mCMV
## 13322 CGTGTACACAGC Trp53 mCMV
## 13349 CGTTGATACTCA Trp53 hBGm
## 13403 AGTCTACCTTCG Trp53 minP
## 13720 GGTCGCTCCATT Trp53 hBGm
## 13742 ACGCACGAGATT Trp53 mCMV
## 13887 CATTCCGCTTGT Trp53 minP
## 14349 TGGTGCACTGTC Trp53 mCMV
## 15447 ACACGTAGCTTA Trp53 mCMV
## 15666 CGTCCTGTAAGA Trp53 mCMV
## 15699 CGCGTCCATCAA Trp53 mCMV
## 15891 AAGCCTGACAAG Trp53 mCMV
## 16430 TCTCCTCTGTGG Trp53 mCMV
## 16926 CACCAAGGCTGA Trp53 mCMV
## 18859 TACGAACTGTGT Trp53 mCMV
## 18869 TCAGTCTACTCT Trp53 mCMV
## 19853 CACCGGAGATCT Trp53 mCMV
## 20265 ATAGAGGCTGAC Trp53 mCMV
## 20648 GGATCATAGTTC Trp53 mCMV
## 20737 GACTATCTAGCA Trp53 mCMV
## 21178 TCTACTGAGTGA Trp53 mCMV
## 21258 GAGCAGGATTGT Trp53 mCMV
## 21327 GCTGTGCAATCG Trp53 mCMV
## 22837 TGTCCGTAACTC Trp53 mCMV
## 23142 TGCTATTAGACC Trp53 mCMV
## 23540 AGTCTATTGGTG Trp53 mCMV
## 23913 CACGCGTCTGAT Trp53 mCMV
## 24108 CGGCCTCGTATT Trp53 hBGm
## 24967 CTACACACCGCT Trp53 mCMV
## 25028 AGGCGCTTAGGT Trp53 mCMV
## 25182 TGGACGCTCTTG Trp53 mCMV
## 25873 TCGTGTACTCCG Trp53 hBGm
## 26543 TCGCAAGTCAGT Trp53 mCMV
## 27779 CCACATCGGAGA Trp53 hBGm
Divide cDNA barcode counts through pDNA barcode counts to get activity
bc_df_cDNA_filt$sample[bc_df_cDNA_filt$sample == "R3_K562_DMSO"] <- "K562_stressed"
bc_df_cDNA_filt$condition[bc_df_cDNA_filt$sample == "K562_stressed"] <- "K562_stressed"## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
paste("Run time: ",format(Sys.time()-StartTime))## [1] "Run time: 6.979267 mins"
getwd()## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/gen2"
date()## [1] "Fri Jul 9 15:03:38 2021"
sessionInfo()## R version 4.0.5 (2021-03-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] pheatmap_1.0.12 PCAtools_2.2.0
## [3] ggrepel_0.9.1 DESeq2_1.30.1
## [5] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [7] MatrixGenerics_1.2.1 matrixStats_0.58.0
## [9] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
## [11] IRanges_2.24.1 S4Vectors_0.28.1
## [13] BiocGenerics_0.36.1 viridis_0.6.0
## [15] viridisLite_0.4.0 grr_0.9.5
## [17] tidyr_1.1.3 LncFinder_1.1.4
## [19] gridExtra_2.3 RColorBrewer_1.1-2
## [21] readr_1.4.0 haven_2.4.1
## [23] ggbeeswarm_0.6.0 plotly_4.9.3
## [25] tibble_3.1.1 dplyr_1.0.5
## [27] vwr_0.3.0 latticeExtra_0.6-29
## [29] lattice_0.20-41 stringdist_0.9.6.3
## [31] GGally_2.1.1 ggpubr_0.4.0
## [33] ggplot2_3.3.3 stringr_1.4.0
## [35] plyr_1.8.6 data.table_1.14.0
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.2.1
## [3] lazyeval_0.2.2 splines_4.0.5
## [5] crosstalk_1.1.1 BiocParallel_1.24.1
## [7] digest_0.6.27 foreach_1.5.1
## [9] htmltools_0.5.1.1 fansi_0.4.2
## [11] memoise_2.0.0 magrittr_2.0.1
## [13] openxlsx_4.2.3 recipes_0.1.16
## [15] annotate_1.68.0 gower_0.2.2
## [17] prettyunits_1.1.1 jpeg_0.1-8.1
## [19] colorspace_2.0-0 blob_1.2.1
## [21] xfun_0.22 crayon_1.4.1
## [23] RCurl_1.98-1.3 jsonlite_1.7.2
## [25] genefilter_1.72.1 survival_3.2-10
## [27] iterators_1.0.13 glue_1.4.2
## [29] gtable_0.3.0 ipred_0.9-11
## [31] zlibbioc_1.36.0 XVector_0.30.0
## [33] seqinr_4.2-5 DelayedArray_0.16.3
## [35] BiocSingular_1.6.0 car_3.0-10
## [37] abind_1.4-5 scales_1.1.1
## [39] DBI_1.1.1 rstatix_0.7.0
## [41] Rcpp_1.0.6 xtable_1.8-4
## [43] progress_1.2.2 dqrng_0.3.0
## [45] rsvd_1.0.5 foreign_0.8-81
## [47] bit_4.0.4 proxy_0.4-25
## [49] lava_1.6.9 prodlim_2019.11.13
## [51] htmlwidgets_1.5.3 httr_1.4.2
## [53] ellipsis_0.3.2 farver_2.1.0
## [55] pkgconfig_2.0.3 reshape_0.8.8
## [57] XML_3.99-0.6 nnet_7.3-15
## [59] sass_0.3.1 locfit_1.5-9.4
## [61] utf8_1.2.1 caret_6.0-86
## [63] labeling_0.4.2 tidyselect_1.1.1
## [65] rlang_0.4.10 reshape2_1.4.4
## [67] AnnotationDbi_1.52.0 cachem_1.0.4
## [69] munsell_0.5.0 cellranger_1.1.0
## [71] tools_4.0.5 generics_0.1.0
## [73] RSQLite_2.2.7 ade4_1.7-16
## [75] broom_0.7.6 fastmap_1.1.0
## [77] evaluate_0.14 yaml_2.2.1
## [79] ModelMetrics_1.2.2.2 knitr_1.33
## [81] bit64_4.0.5 zip_2.1.1
## [83] purrr_0.3.4 sparseMatrixStats_1.2.1
## [85] nlme_3.1-152 compiler_4.0.5
## [87] beeswarm_0.3.1 curl_4.3
## [89] png_0.1-7 e1071_1.7-6
## [91] ggsignif_0.6.1 geneplotter_1.68.0
## [93] bslib_0.2.4 stringi_1.5.3
## [95] highr_0.9 forcats_0.5.1
## [97] Matrix_1.3-2 vctrs_0.3.8
## [99] pillar_1.6.0 lifecycle_1.0.0
## [101] jquerylib_0.1.4 irlba_2.3.3
## [103] cowplot_1.1.1 bitops_1.0-7
## [105] R6_2.5.0 rio_0.5.26
## [107] vipor_0.4.5 codetools_0.2-18
## [109] MASS_7.3-53.1 assertthat_0.2.1
## [111] withr_2.4.2 GenomeInfoDbData_1.2.4
## [113] mgcv_1.8-34 hms_1.0.0
## [115] beachmat_2.6.4 grid_4.0.5
## [117] rpart_4.1-15 timeDate_3043.102
## [119] class_7.3-18 DelayedMatrixStats_1.12.3
## [121] rmarkdown_2.7 carData_3.0-4
## [123] pROC_1.17.0.1 lubridate_1.7.10